Job ID = 1302756 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,894,161 reads read : 25,894,161 reads written : 25,894,161 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:25 25894161 reads; of these: 25894161 (100.00%) were unpaired; of these: 1020972 (3.94%) aligned 0 times 14260279 (55.07%) aligned exactly 1 time 10612910 (40.99%) aligned >1 times 96.06% overall alignment rate Time searching: 00:15:25 Overall time: 00:15:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 15486791 / 24873189 = 0.6226 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 20:44:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 20:44:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:44:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:44:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 20:44:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:44:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:44:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 20:44:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:44:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:44:10: 1000000 INFO @ Mon, 03 Jun 2019 20:44:11: 1000000 INFO @ Mon, 03 Jun 2019 20:44:11: 1000000 INFO @ Mon, 03 Jun 2019 20:44:18: 2000000 INFO @ Mon, 03 Jun 2019 20:44:19: 2000000 INFO @ Mon, 03 Jun 2019 20:44:19: 2000000 INFO @ Mon, 03 Jun 2019 20:44:26: 3000000 INFO @ Mon, 03 Jun 2019 20:44:27: 3000000 INFO @ Mon, 03 Jun 2019 20:44:27: 3000000 INFO @ Mon, 03 Jun 2019 20:44:34: 4000000 INFO @ Mon, 03 Jun 2019 20:44:35: 4000000 INFO @ Mon, 03 Jun 2019 20:44:36: 4000000 INFO @ Mon, 03 Jun 2019 20:44:42: 5000000 INFO @ Mon, 03 Jun 2019 20:44:44: 5000000 INFO @ Mon, 03 Jun 2019 20:44:45: 5000000 INFO @ Mon, 03 Jun 2019 20:44:50: 6000000 INFO @ Mon, 03 Jun 2019 20:44:53: 6000000 INFO @ Mon, 03 Jun 2019 20:44:54: 6000000 INFO @ Mon, 03 Jun 2019 20:44:58: 7000000 INFO @ Mon, 03 Jun 2019 20:45:02: 7000000 INFO @ Mon, 03 Jun 2019 20:45:02: 7000000 INFO @ Mon, 03 Jun 2019 20:45:06: 8000000 INFO @ Mon, 03 Jun 2019 20:45:10: 8000000 INFO @ Mon, 03 Jun 2019 20:45:10: 8000000 INFO @ Mon, 03 Jun 2019 20:45:14: 9000000 INFO @ Mon, 03 Jun 2019 20:45:17: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 20:45:17: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 20:45:17: #1 total tags in treatment: 9386398 INFO @ Mon, 03 Jun 2019 20:45:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:45:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:45:17: #1 tags after filtering in treatment: 9386398 INFO @ Mon, 03 Jun 2019 20:45:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:45:17: #1 finished! INFO @ Mon, 03 Jun 2019 20:45:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:45:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:45:18: #2 number of paired peaks: 808 WARNING @ Mon, 03 Jun 2019 20:45:18: Fewer paired peaks (808) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 808 pairs to build model! INFO @ Mon, 03 Jun 2019 20:45:18: start model_add_line... INFO @ Mon, 03 Jun 2019 20:45:18: start X-correlation... INFO @ Mon, 03 Jun 2019 20:45:18: end of X-cor INFO @ Mon, 03 Jun 2019 20:45:18: #2 finished! INFO @ Mon, 03 Jun 2019 20:45:18: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 20:45:18: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 20:45:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.05_model.r WARNING @ Mon, 03 Jun 2019 20:45:18: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:45:18: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 20:45:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 20:45:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:45:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:45:19: 9000000 INFO @ Mon, 03 Jun 2019 20:45:19: 9000000 INFO @ Mon, 03 Jun 2019 20:45:23: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 20:45:23: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 20:45:23: #1 total tags in treatment: 9386398 INFO @ Mon, 03 Jun 2019 20:45:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:45:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:45:23: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 20:45:23: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 20:45:23: #1 total tags in treatment: 9386398 INFO @ Mon, 03 Jun 2019 20:45:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:45:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:45:23: #1 tags after filtering in treatment: 9386398 INFO @ Mon, 03 Jun 2019 20:45:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:45:23: #1 finished! INFO @ Mon, 03 Jun 2019 20:45:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:45:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:45:23: #1 tags after filtering in treatment: 9386398 INFO @ Mon, 03 Jun 2019 20:45:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:45:23: #1 finished! INFO @ Mon, 03 Jun 2019 20:45:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:45:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:45:24: #2 number of paired peaks: 808 WARNING @ Mon, 03 Jun 2019 20:45:24: Fewer paired peaks (808) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 808 pairs to build model! INFO @ Mon, 03 Jun 2019 20:45:24: start model_add_line... INFO @ Mon, 03 Jun 2019 20:45:24: start X-correlation... INFO @ Mon, 03 Jun 2019 20:45:24: end of X-cor INFO @ Mon, 03 Jun 2019 20:45:24: #2 finished! INFO @ Mon, 03 Jun 2019 20:45:24: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 20:45:24: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 20:45:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.10_model.r WARNING @ Mon, 03 Jun 2019 20:45:24: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:45:24: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 20:45:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 20:45:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:45:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:45:24: #2 number of paired peaks: 808 WARNING @ Mon, 03 Jun 2019 20:45:24: Fewer paired peaks (808) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 808 pairs to build model! INFO @ Mon, 03 Jun 2019 20:45:24: start model_add_line... INFO @ Mon, 03 Jun 2019 20:45:24: start X-correlation... INFO @ Mon, 03 Jun 2019 20:45:24: end of X-cor INFO @ Mon, 03 Jun 2019 20:45:24: #2 finished! INFO @ Mon, 03 Jun 2019 20:45:24: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 20:45:24: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 20:45:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.20_model.r WARNING @ Mon, 03 Jun 2019 20:45:24: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:45:24: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 20:45:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 20:45:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:45:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:45:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:45:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:45:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:45:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:45:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:45:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.05_summits.bed INFO @ Mon, 03 Jun 2019 20:45:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3279 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:46:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:46:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:46:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.10_summits.bed INFO @ Mon, 03 Jun 2019 20:46:06: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1653 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:46:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:46:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:46:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4933892/SRX4933892.20_summits.bed INFO @ Mon, 03 Jun 2019 20:46:08: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1295 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。